In the spIBDerverse app, there are three ways to get data into the app.
Load examples
Built into the spIBDerverse package are numerous example
neworks that can be loaded into the app using the
load_examples() function.
example <- load_example()
example
#> IGRAPH 22f3232 UN-- 40 110 --
#> + attr: genetic_sex (v/c), site (v/c), name (v/n), .degree (v/n),
#> | .closeness (v/n), .betweenness (v/n), .eigencentrality (v/n), lat
#> | (v/n), long (v/n), wij (e/n), edge_type (e/c)
#> + edges from 22f3232 (vertex names):
#> [1] 1-- 9 1--13 1--14 1--15 1--17 1--19 1--20 1--25 1--28 2-- 5
#> [11] 2--14 2--24 2--26 2--28 2--36 3-- 4 3-- 6 3--16 3--24 3--34
#> [21] 3--39 4-- 8 4--10 4--14 4--27 4--30 4--36 4--37 5-- 7 5-- 9
#> [31] 5--11 5--15 5--20 5--25 5--31 5--33 7-- 9 7--12 7--13 7--23
#> [41] 7--25 7--38 8--14 9--10 9--11 9--16 9--23 9--25 9--26 9--38
#> [51] 10--34 10--38 10--40 11--12 11--29 11--33 11--40 12--29 12--32 12--33
#> + ... omitted several edgesIt will return a message if you ask for a dataset that does not exist.
load_example("bob")
#> That data does not exist
#> NULLLoad an IBD network
This will use two files:
- an IBD file which gives the edges, and
- an META file which has node information:
ibd_file <- fs::path_package(
"extdata/example-ibd-data.tsv",
package = "spIBDerverse"
)
ibd_file |> readr::read_tsv() |> dplyr::slice(1:5)
#> Rows: 4789 Columns: 11
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (2): iid1, iid2
#> dbl (9): max_IBD, sum_IBD>8, n_IBD>8, sum_IBD>12, n_IBD>12, sum_IBD>16, n_IB...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> # A tibble: 5 × 11
#> iid1 iid2 max_IBD `sum_IBD>8` `n_IBD>8` `sum_IBD>12` `n_IBD>12` `sum_IBD>16`
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 KUP0… KUP0… 284. 3403. 22 3403. 22 3403.
#> 2 RKC0… RKC0… 284. 3399. 23 3399. 23 3399.
#> 3 RKF2… RKC0… 269. 3394. 22 3394. 22 3394.
#> 4 RKF1… RKF1… 284. 3390. 22 3390. 22 3390.
#> 5 RKF1… RKC0… 284. 3389. 23 3389. 23 3389.
#> # ℹ 3 more variables: `n_IBD>16` <dbl>, `sum_IBD>20` <dbl>, `n_IBD>20` <dbl>
meta_file <- fs::path_package(
"extdata/example-meta-data.tsv",
package = "spIBDerverse"
)
meta_file |> readr::read_tsv() |> dplyr::slice(1:5)
#> Rows: 328 Columns: 16
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (10): iid, Archaeological_ID, Master_ID, Projects, Locality, Province, C...
#> dbl (6): frac_gp, frac_missing, frac_het, n_cov_snp, Latitude, Longitude
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> # A tibble: 5 × 16
#> iid frac_gp frac_missing frac_het n_cov_snp Archaeological_ID Master_ID
#> <chr> <dbl> <dbl> <dbl> <dbl> <chr> <chr>
#> 1 RKO006 0.953 0.0340 0.269 1154253 190/388 RKO006
#> 2 RKO002 0.953 0.0340 0.269 1043584 331/441 RKO002
#> 3 RKF270 0.951 0.0340 0.260 891830 621/746 RKF270
#> 4 RKF273 0.932 0.0340 0.271 831942 623/748 RKF273
#> 5 RKO003 0.927 0.0340 0.271 939881 543/669 RKO003
#> # ℹ 9 more variables: Projects <chr>, Locality <chr>, Province <chr>,
#> # Country <chr>, Latitude <dbl>, Longitude <dbl>, date <chr>,
#> # date_type <chr>, imputation_type <chr>The IBD file must have two columns iid1 and
iid2 else you can not create the IBD network, while the
META file must have a column called iid.
load_ibd_network(ibd_file, meta_file)
#> IGRAPH 23b8fba UN-- 328 1712 --
#> + attr: name (v/c), frac_gp (v/n), frac_missing (v/n), frac_het (v/n),
#> | n_cov_snp (v/n), Archaeological_ID (v/c), Master_ID (v/c), Projects
#> | (v/c), Locality (v/c), Province (v/c), Country (v/c), Latitude (v/n),
#> | Longitude (v/n), date (v/c), date_type (v/c), imputation_type (v/c),
#> | .degree (v/n), .closeness (v/n), .betweenness (v/n), .eigencentrality
#> | (v/n), frac_gp1 (e/n), frac_gp2 (e/n), max_ibd (e/n), sum_ibd_8
#> | (e/n), n_ibd_8 (e/n), sum_ibd_12 (e/n), n_ibd_12 (e/n), sum_ibd_16
#> | (e/n), n_ibd_16 (e/n), sum_ibd_20 (e/n), n_ibd_20 (e/n), wij (e/n)
#> + edges from 23b8fba (vertex names):
#> [1] KUP007--KUP023 RKC013--RKC029 RKC031--RKF238 RKF195--RKF196 RKC020--RKF142
#> + ... omitted several edges